BMRB Entry 34219

Name: Solution structure of the MRH domain of Yos9 complexed with alpha3,alpha6-Man5
Published: 2019-01-28

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PDB ID: 6f9a
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR34219
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: Solution structure of the MRH domain of Yos9 complexed with alpha3,alpha6-Man5 PubMed: 30066206

Deposition date: 2017-12-14 Original release date: 2019-01-28

Authors: Kniss, A.; Kazemi, S.; Lohr, F.; Guntert, P.; Dotsch, V.

Citation: Kniss, Andreas; Kazemi, Sina; Lohr, Frank; Berger, Maren; Rogov, Vladimir; Guntert, Peter; Sommer, Thomas; Jarosch, Ernst; Dotsch, Volker. "Structural investigation of glycan recognition by the ERAD quality control lectin Yos9" J. Biomol. NMR 72, 1-10 (2018).

Assembly members:
entity_1, polymer, 162 residues, 18328.627 Da.

Natural source: Common Name: Baker's yeast Taxonomy ID: 4932 Superkingdom: Eukaryota Kingdom: Fungi Genus/species: Saccharomyces cerevisiae

Experimental source: Production method: recombinant technology Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: GASNSEKTALLTKTLNQGVK TIFDKLNERCIFYQAGFWIY EYCPGIEFVQFHGRVNTKTG EIVNRDESLVYRLGKPKANV EEREFELLYDDVGYYISEII GSGDICDVTGAERMVEIQYV CGGSNSGPSTIQWVRETKIC VYEAQVTIPELCNLELLAKN ED

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	676
15N chemical shifts	148
1H chemical shifts	1067

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 162 residues - 18328.627 Da.

1

GLY

ALA

SER

ASN

SER

GLU

LYS

THR

ALA

LEU

2

LEU

THR

LYS

THR

LEU

ASN

GLN

GLY

VAL

LYS

3

THR

ILE

PHE

ASP

LYS

LEU

ASN

GLU

ARG

CYS

4

ILE

PHE

TYR

GLN

ALA

GLY

PHE

TRP

ILE

TYR

5

GLU

TYR

CYS

PRO

GLY

ILE

GLU

PHE

VAL

GLN

6

PHE

HIS

GLY

ARG

VAL

ASN

THR

LYS

THR

GLY

7

GLU

ILE

VAL

ASN

ARG

ASP

GLU

SER

LEU

VAL

8

TYR

ARG

LEU

GLY

LYS

PRO

LYS

ALA

ASN

VAL

9

GLU

ARG

GLU

PHE

GLU

LEU

TYR

ASP

10

ASP

VAL

GLY

TYR

ILE

SER

GLU

ILE

11

GLY

SER

GLY

ASP

ILE

CYS

ASP

VAL

THR

GLY

12

ALA

GLU

ARG

MET

VAL

GLU

ILE

GLN

TYR

VAL

13

CYS

GLY

SER

ASN

SER

GLY

PRO

SER

THR

14

ILE

GLN

TRP

VAL

ARG

GLU

THR

LYS

ILE

CYS

15

VAL

TYR

GLU

ALA

GLN

VAL

THR

ILE

PRO

GLU

16

LEU

CYS

ASN

LEU

GLU

LEU

ALA

LYS

ASN

17

GLU

ASP

Samples:

sample_1: MRH domain of Yos9, [U-98% 13C; U-98% 15N], 0.55 mM; alpha3,alpha6-Man5 8.25 mM

sample_2: MRH domain of Yos9, [U-98% 13C; U-98% 15N], 1 mM; alpha3,alpha6-Man5 15 mM

sample_conditions_1: ionic strength: 50 mM; pH: 7.0; pressure: 1 atm; temperature: 303 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HN(COCA)CB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H TOCSY	sample_1	isotropic	sample_conditions_1
3D 13C TOCSY	sample_1	isotropic	sample_conditions_1
2D(HB)CB(CGCD)HD	sample_1	isotropic	sample_conditions_1
2D (H)CB(CGCC)H TOCSY	sample_1	isotropic	sample_conditions_1

Software:

SPARKY v3.13, Goddard - chemical shift assignment

CYANA v3.9, Guntert, P. - structure calculation

OPAL, Luginbuhl, Guntert, Billeter and Wuthrich - refinement

NMR spectrometers:

Bruker Avance 600 MHz
Bruker Avance 700 MHz
Bruker Avance 950 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts